User: Chironex

gravatar for Chironex
Chironex20
Reputation:
20
Status:
New User
Location:
rome
Last seen:
1 month, 2 weeks ago
Joined:
10 months, 3 weeks ago
Email:
o************@gmail.com

Posts by Chironex

<prev • 45 results • page 1 of 5 • next >
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correlation between element-gene
... I have two matrix identical in N° of rows and columns. In the first matrix rows indicate transposable elements and columns indicate samples. the matrix show the degree of expression of each element in samples: M1 <- elements ova testes re ...
R correlation written 8 weeks ago by Chironex20
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tool to detect the role of transposon on genic regulation
... Hello everyone, I'm looking for an advice. I found some transposable elements with repeatmaskers in an assembled genome. what interests me now is to check the position of some transposons in different genes to try to understand their role on gene expression. could you recommend a program in R that i ...
R transposon written 5 months ago by Chironex20
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Comment: C: normalization with RPKM
... Stringtie is not implemented in R, right? ...
written 6 months ago by Chironex20
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Comment: C: normalization with RPKM
... Is it usable even if elements are not genes, but transposon? the gtf file of featurecounts is the output of repeatmasker analysis ...
written 6 months ago by Chironex20
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normalization with RPKM
... hello! I'm very i difficult with normalization of my data. I was searching for transposable elements in my genome, and after this step, I made counts of reads in some transcripts. I produced something like that: head(table_tissues_filtered_TE) Lengths ova testes lobe retin ...
normalization transposon data rna-seq rpkm written 6 months ago by Chironex20 • updated 6 months ago by darbinator190
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Comment: C: repeatmasker species setting
... ~/RM/RepeatMasker/util$ ls -l totale 204 -rwxr-xr-x 1 fragua fragua 4622 nov 21 2018 buildRMLibFromEMBL.pl -rwxr-xr-x 1 fragua fragua 22868 nov 21 2018 buildSummary.pl -rwxr-xr-x 1 fragua fragua 10430 nov 21 2018 calcDivergenceFromAlign.pl -rwxr-xr-x 1 fragua fragua 20607 ...
written 6 months ago by Chironex20
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Comment: C: repeatmasker species setting
... If I put `~/RM/RepeatMasker/util$ queryRepeatDatabase.pl -h` , it says to me queryRepeatDatabase.pl: command not found ...
written 6 months ago by Chironex20
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Comment: C: repeatmasker species setting
... okay, thank you for your help! ...
written 6 months ago by Chironex20
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Comment: C: repeatmasker species setting
... okay, but repeatmasker will be able to recognize the library created by myself finding transposable elements? I've tried using Repeatscout, but the results didn't are the expected. Repeatmodeler is different? ...
written 6 months ago by Chironex20
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repeatmasker species setting
... hello! I'm working with a genome of cephalopoda. Firstly, I ran Repeatmasker with this input /home/RM/RepeatMasker -s -gff OB150DEC_2.fa to analyze the genome assuming that the specie is homo sapiens. I'm not sure that it is correct, because I suppose that transposable elements could be dif ...
genome repeatmasker written 6 months ago by Chironex20 • updated 6 months ago by Juke-343.2k

Latest awards to Chironex

Scholar 5 months ago, created an answer that has been accepted. For C: error RepeatMasker Installation

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